The Waterloo to Weymouth services have a waypoint before their last stop (either Ardhurst or Clapham Junction). These are treated as the stop after them, here London Waterloo, which is timetabled. As a result trains stop and wait for schedule as if they were at Waterloo, then continue to the next stop after Waterloo.
.sve: https://drive.google.com/file/d/0ByLSSg3gXTz-VGF2S3VnbHpodzQ/view?usp=sharing
Thank you for the report - I think that I have now found and fixed this. Would you be able to re-test? I should be most grateful.